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The crystal structure of the antimycin pathway standalone ketoreductase, AntM, in complex with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298.15 0.1 M Tris, pH 8.5, 5% w/v PEG 8K, 20% v/v PEG 300, 10% v/v glycerol
Crystal Properties Matthews coefficient Solvent content 2.33 47.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.223 α = 90 b = 92.223 β = 90 c = 113.751 γ = 120
Symmetry Space Group P 62 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2018-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.7 65.36 100 1 24.7 21.2 33683
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.958
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4osp 1.7 65.36 32045 1638 99.953 0.2 0.1987 0.1987 0.2242 0.2244 38.772
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.67 0.835 1.67 -5.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.557 r_dihedral_angle_4_deg 17.404 r_dihedral_angle_3_deg 12.985 r_dihedral_angle_1_deg 6.577 r_lrange_other 6.236 r_lrange_it 6.234 r_scangle_it 5.292 r_scangle_other 5.29 r_mcangle_it 4.077 r_mcangle_other 4.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.557 r_dihedral_angle_4_deg 17.404 r_dihedral_angle_3_deg 12.985 r_dihedral_angle_1_deg 6.577 r_lrange_other 6.236 r_lrange_it 6.234 r_scangle_it 5.292 r_scangle_other 5.29 r_mcangle_it 4.077 r_mcangle_other 4.068 r_scbond_it 3.78 r_scbond_other 3.778 r_mcbond_it 3.305 r_mcbond_other 3.291 r_angle_other_deg 2.414 r_angle_refined_deg 1.657 r_symmetry_nbd_other 0.222 r_nbd_other 0.221 r_nbd_refined 0.218 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.124 r_symmetry_xyhbond_nbd_other 0.123 r_symmetry_nbd_refined 0.107 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.069 r_bond_other_d 0.036 r_gen_planes_other 0.013 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1810 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement Aimless data reduction Aimless data scaling PHASER phasing